This is a bit difficult to explain, but I will try.

If you have non-recessed chambers and load one round and fire it (a heavy recoiling pistol like a .454 or .475) with no other cases in the cylinder to support the loading gate to keep it from flexing as far, you may eventually damage the loading gate. If the cylinder is recessed and you have no other cases in the cylinder than the one you are firing, the loading gate can flex no further than a non-recessed cylinder with a full load of cases. It closes the gap in other words, meaning you can shoot it one round in the cylinder at a time without any negative consequences.

Freedom counter bores their cylinders as does Magnum Research on their BFRs. Some custom smiths do, some don't. You won't get a custom SA revolver from Jack Huntington that isn't counter-bored, nor from Hamilton Bowen if I can recall.